All of you in Fay's path are in my prayers, for you, your animals, & your property. I pray she will weaken and have minimal impact!
I had much fewer chickens during the year we had the awful twin hurricanes Francis & Jeanne hitting us in quick succession, and again the next year when we had a visit from Wilma. Not knowing how my coops would hold up in hurricane-force winds and not wanting to lament afterwards "Oh, if ONLY I had..." I played it very safe and brought all my flock indoors.
I layered newspaper & straw in the back bathroom and brought all the chickens in during the storm. It added some much-needed comedic relief to peek in there and see them pecking & scratching around the fixtures. Though it wasn't quite so amusing early the next morning when the roos began to crow, their voices echoing off the tiles.
The flock was bigger the next year during Wilma, but I still brought them all indoors. Some I put in the bathroom again, others I stuffed in wire cages, and the rest were put in cardboard banana boxes and stacked in the hall. I figured they would be all right without food or water for a limited number of hours, just during the worst part of the weather. It was dark and quiet & they mostly slept.
The worst part of the hurricane rarely lasts more than 12 hours, and once it's passed the birds can go outside again.
Of course you may have to make other housing arrangements for your flock if your coops or pens have sustained damage or blown away, or if their runs are under too much water. But otherwise, it's just like any other heavy rainstorm.
I need to make plans for my much larger flock in case Palm Beach County gets a hurricane this year. I have 53 baby chicks, 66 adult chickens, 3 guinea hens, 5 ducks, 3 snakes, a parakeet, and 2 tanks of feeder mice that all live outdoors or out on the screened patio. And 3 children who fully expect me to keep them and ALL of the animals safe through any storm.
Fay, Fay, go away, don't come back on any day!